int i;
t_ho_params hop;
t_lj_params ljp;
+ t_tersoff_params tp;
double s,e;
memset(moldyn,0,sizeof(t_moldyn));
moldyn->mwrite=atoi(argv[++i]);
strncpy(moldyn->mfb,argv[++i],64);
break;
- case 'D':
- moldyn->dwrite=atoi(argv[++i]);
- strncpy(moldyn->dfb,argv[++i],64);
- break;
case 'S':
moldyn->swrite=atoi(argv[++i]);
strncpy(moldyn->sfb,argv[++i],64);
if(moldyn->swrite)
moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
- if(moldyn->dwrite) {
- moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->dfd<0) {
- perror("[moldyn] dfd open");
- return moldyn->dfd;
- }
- write(moldyn->dfd,moldyn,sizeof(t_moldyn));
- moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
- }
-
if((moldyn->vwrite)&&(vis)) {
moldyn->visual=vis;
visual_init(vis,moldyn->vfb);
}
}
+ lc->dnlc=count2;
+ lc->countn=27;
+
return count2;
}
write(fd,moldyn->atom,
moldyn->count*sizeof(t_atom));
}
+ close(fd);
}
}
- if(d) {
- if(!(i%d))
- write(moldyn->dfd,moldyn->atom,
- moldyn->count*sizeof(t_atom));
-
- }
if(v) {
if(!(i%v)) {
visual_atoms(moldyn->visual,i*moldyn->tau,
/* forces depending on chosen potential */
printf("calc potential/force ...\n");
- moldyn->potential_force_function(moldyn);
+ potential_force_calc(moldyn);
+ //moldyn->potential_force_function(moldyn);
printf("done\n");
for(i=0;i<count;i++) {
*
*/
+/* generic potential and force calculation */
+
+#define CREATE_CELL_LIST(nb_list) \
+ link_cell_neighbour_index(moldyn,\
+ (atom[i].r.x+moldyn->dim.x/2)/lc->x,\
+ (atom[i].r.y+moldyn->dim.y/2)/lc->y,\
+ (atom[i].r.z+moldyn->dim.z/2)/lc->z,\
+ nb_list);
+
+
+int potential_force_calc(t_moldyn *moldyn) {
+
+ int i,count;
+ t_atom *atom;
+ t_linkcell *lc;
+ t_list neighbour[27];
+ t_list *this;
+ double u;
+
+ count=moldyn->count;
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ /* reset energy */
+ u=0.0;
+
+ for(i=0;i<count;i++) {
+
+ /* reset force */
+ v3_zero(&(atom[i].f));
+
+ /* single particle potential/force */
+ if(moldyn->status&MOLDYN_STAT_1BP)
+ moldyn->pf_func1b(moldyn,&(atom[i]));
+
+ /* 2 body pair potential/force */
+ if(moldyn->status&MOLDYN_STAT_2BP) {
+
+ CREATE_CELL_LIST(neighbour);
+
+ /*
+ * processing cell of atom i
+ * => no need to check for empty list
+ * (1 element at minimum)
+ */
+
+ this=&(neighbour[0]);
+ list_reset(this);
+ do {
+ btom=this->current->data;
+ if(btom!=&(atom[i]))
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),btom);
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /*
+ * direct neighbour cells
+ * => no boundary condition check necessary
+ */
+ for(j=0;j<lc->dnlc;j++) {
+ this=&(neighbour[j]);
+ list_reset(this);
+ if(this->start!=NULL) {
+ do {
+ btom=this->current->data;
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),
+ btom);
+ } while(list_next(this)!=\
+ L_NO_NEXT_ELEMENT);
+ }
+
+ /*
+ * neighbour cells due to periodic bc
+ * => check boundary conditions
+ */
+ for(j=lc->dnlc;j<lc->countn;j++) {
+ this=&(neighbour[j]);
+ list_reset(this);
+ if(this->start!=NULL) {
+ do {
+ btom=this->current->data;
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),
+ btom);
+
+ }
+
+ }
+
+ return 0;
+}
+
+
/* harmonic oscillator potential and force */
int harmonic_oscillator(t_moldyn *moldyn) {
double x,y,z; /* the actual cell lengthes */
t_list *subcell; /* pointer to the cell lists */
int dnlc; /* direct neighbour lists counter */
+ int countn; /* amount of neighbours */
} t_linkcell;
#include "visual/visual.h"
-# moldyn properties structure */
+# moldyn structure */
typedef struct s_moldyn {
int count; /* total amount of atoms */
t_atom *atom; /* pointer to the atoms */
+
t_3dvec dim; /* dimensions of the simulation volume */
- /* potential, force & parameters */
- /* potential force funtion created by the user */
- int (*potential_force_function)(struct s_moldyn *moldyn);
+ /* potential force function pointer and parameters */
+ int (*pf_func1b)(struct s_moldyn *,t_atom *);
+ int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+ int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+ //int (*potential_force_function)(struct s_moldyn *moldyn);
void *pot_params; /* parameters describing the potential */
- double cutoff;
- double cutoff_square;
- /* linked list / cell method */
- t_linkcell lc;
- /* temperature */
- double t;
- /* integration of newtons equations */
+ double cutoff; /* cutoff radius */
+ double cutoff_square; /* square of the cutoff radius */
+
+ t_linkcell lc; /* linked cell method */
+
+ double t; /* temperature */
+
+ /* integration function pointer */
int (*integrate)(struct s_moldyn *moldyn);
- int time_steps;
- double tau;
- double tau_square;
- /* energy */
- double energy;
- /* logging & visualization */
- t_visual vis;
- unsigned char lvstat;
- unsigned int ewrite;
- char efb[64];
- int efd;
- unsigned int mwrite;
- char mfb[64];
- int mfd;
- unsigned int swrite;
- char sfb[64];
- int sfd;
- unsigned int dwrite;
- char dfb[64];
- int dfd;
- unsigned int vwrite;
- char vfb[64];
- void *visual;
- /* moldyn general status */
- unsigned char status;
- /* random */
- t_random random;
+ int time_steps; /* amount of iterations */
+ double tau; /* delta t */
+ double tau_square; /* delta t squared */
+
+ double energy; /* energy */
+
+ t_visual vis; /* visualization/log/save interface structure */
+ unsigned char lvstat; /* log & vis properties */
+ unsigned int ewrite; /* how often to log energy */
+ char efb[64]; /* energy log filename */
+ int efd; /* fd for energy log */
+ unsigned int mwrite; /* how often to log momentum */
+ char mfb[64]; /* momentum log filename */
+ int mfd; /* fd for momentum log */
+ unsigned int vwrite; /* how often to visualize atom information */
+ char vfb[64]; /* visualization file name base */
+ void *visual; /* pointer (hack!) */
+ unsigned int swrite; /* how often to create a save file */
+
+ unsigned char status; /* general moldyn properties */
+
+ t_random random; /* random interface */
} t_moldyn;
+#define MOLDYN_LVSTAT_TOTAL_E 0x01
+#define MOLDYN_LVSTAT_TOTAL_M 0x02
+#define MOLDYN_LVSTAT_SAVE 0x04
+#define MOLDYN_LVSTAT_VISUAL 0x08
+#define MOLDYN_LVSTAT_INITIALIZED 0x10
+
+#define MOLDYN_STAT_1BP 0x01
+#define MOLDYN_STAT_2BP 0x02 /* define for pair potentials */
+#define MOLDYN_STAT_3BP 0x04 /* define for 3 body pot */
+#define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */
+#define MOLDYN_STAT_PBY 0x10 /* y */
+#define MOLDYN_STAT_PBZ 0x20 /* and z direction */
+
typedef struct s_ho_params {
double spring_constant;
double equilibrium_distance;
/* general defines */
-#define MOLDYN_LVSTAT_TOTAL_E 0x01
-#define MOLDYN_LVSTAT_TOTAL_M 0x02
-#define MOLDYN_LVSTAT_SAVE 0x04
-#define MOLDYN_LVSTAT_DUMP 0x08
-#define MOLDYN_LVSTAT_VISUAL 0x10
-#define MOLDYN_LVSTAT_INITIALIZED 0x80
-
-#define MOLDYN_STAT_POTENTIAL 0x01
-#define MOLDYN_STAT_FORCE 0x02
-
#define MOLDYN_TEMP 273.0
#define MOLDYN_TAU 1.0e-15
#define MOLDYN_CUTOFF 10.0e-9
#define MOLDYN_RUNS 1000000
#define MOLDYN_INTEGRATE_VERLET 0x00
-#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
#define MOLDYN_POTENTIAL_HO 0x00
#define MOLDYN_POTENTIAL_LJ 0x01
-#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
/* phsical values */
projects / physik / posic.git / commitdiff